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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgaggcaaacgatcttatgttatgtttcaaatctagaggatgtcattagattagtgctgttgcttgctactgagacatttcattgttttcaacgtacagGATTGGATTCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCCAGGAAAG

Basic information

species Physcomitrella patens
transcript PP1S71_187V6.1
intron # 2
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|208390856|gb|DC942202.1|DC942202
EST:     ATTGCGGCCAAGTTGGAGATCATGGAGCCTTGCTGCAGTGTCAAGGATAG                         GATTGGATTCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCC
genomic: ATTGCGGCCAAGTTGGAGATCATGGAGCCTTGCTGCAGTGTCAAGGATAGgtgtgcttct ... caacgtacagGATTGGATTCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCC
EST: gi|18330835|gb|BJ162841.1|BJ162841
EST:     ATTGCGGCCAAGTTGGAGATCATGGAGCCTTGCTGCAGTGTCAAGGATAG                         GATTGGATTCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATT
genomic: ATTGCGGCCAAGTTGGAGATCATGGAGCCTTGCTGCAGTGTCAAGGATAGgtgtgcttct ... caacgtacagGATTGGATTCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATT
EST: gi|100385278|gb|BY950870.1|BY950870
EST:     ATTGCGGCCAAGTTGGAGATCATGGAGCCTTGCTGCAGTGTCAAGGATAG                         GATTGGATTCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCC
genomic: ATTGCGGCCAAGTTGGAGATCATGGAGCCTTGCTGCAGTGTCAAGGATAGgtgtgcttct ... caacgtacagGATTGGATTCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCC
EST: gi|100409032|gb|BY991846.1|BY991846
EST:     ATTGCGGCCAAGTTGGAGATCATGGAGCCTTGCTGCAGTGTCAAGGATAG                         GATTGGATTCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCC
genomic: ATTGCGGCCAAGTTGGAGATCATGGAGCCTTGCTGCAGTGTCAAGGATAGgtgtgcttct ... caacgtacagGATTGGATTCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCC
EST: gi|162171775|gb|FC348951.1|FC348951
EST:     ATTGCGGCCAAGTTGGAGATCATGGAGCCTTGCTGCAGTGTCAAGGATAG                         GATTGGATTCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCC
genomic: ATTGCGGCCAAGTTGGAGATCATGGAGCCTTGCTGCAGTGTCAAGGATAGgtgtgcttct ... caacgtacagGATTGGATTCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCC
EST: gi|162184261|gb|FC359683.1|FC359683
EST:     ATTGCGGCCAAGTTGGAGATCATGGAGCCTTGCTGCAGTGTCAAGGATAG                         GATTGGATTCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCC
genomic: ATTGCGGCCAAGTTGGAGATCATGGAGCCTTGCTGCAGTGTCAAGGATAGgtgtgcttct ... caacgtacagGATTGGATTCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCC
EST: gi|100363590|gb|BY966464.1|BY966464
EST:     ATTGCGGCCAAGTTGGAGATCATGGAGCCTTGCTGCAGTGTCAAGGATAG                         GATTGGATTCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCC
genomic: ATTGCGGCCAAGTTGGAGATCATGGAGCCTTGCTGCAGTGTCAAGGATAGgtgtgcttct ... caacgtacagGATTGGATTCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCC
EST: gi|208349485|gb|DC905623.1|DC905623
EST:     ATTGCGGCCAAGTTGGAGATCATGGAGCCTTGCTGCAGTGTCAAGGATAG                         GATTGGATTCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCC
genomic: ATTGCGGCCAAGTTGGAGATCATGGAGCCTTGCTGCAGTGTCAAGGATAGgtgtgcttct ... caacgtacagGATTGGATTCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attagattagtgctgttgcttgctactgagacatttcattgttttcaacgtacagGATTGGATTCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCCAGGAAAG
                                      ttgttttc  CT-rich tract
 atttcatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggcaaacgatcttatgttatgtttcaaatctagaggatgtcattagattagtgctgttgcttgctactgagacatttcattgttttcaacgtacagGATTGGATTCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCCAGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG